Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.
I don't know what software you are using but it sounds like there is an atom with an unfilled valence (i.e. not enough bonds attached to it, but also hasn't been assigned a negative charge). Or it might be that it is expecting a specific functinality on the atom but sees a hydrogen instead (i.e. it expects methyl group but there is a hydrogen instead.
It all depends on the specific software you are using and the test it is performing that your molecule is failing, but certainly at first glance it appears as though part of you molecule is incorrect in some way.
Mr.Jason Smith, I am using Gromacs 4.5.3 for pH dependent simulation.
Hi.
Did you use pdb2gmx to build your initial simulation files? If so, did you get any warnings?
You could use the "-ter" card to interactively set your termini as you wish (e.g. charged or neutral). If you do so, pdb2gmx would automatically correct problems in the terminal residues.
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